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minor change, bamFiles comes from the input list, not the script 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4170 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-08-31 16:03:35 +00:00
parent 1a14dbee1e
commit 5e710050d6
1 changed files with 1 additions and 1 deletions
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2
scala/qscript/fullCallingPipeline.q
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@ -156,7 +156,7 @@ class fullCallingPipeline extends QScript {
var indelGenotypers = List.empty[IndelGenotyperV2 with CommandLineGATKArgs] var indelGenotypers = List.empty[IndelGenotyperV2 with CommandLineGATKArgs]
var loopNo = 0 var loopNo = 0
var priority = "" var priority = ""
for ( bam <- qscript.bamFiles ) { for ( bam <- bamFiles ) {
val indel = new IndelGenotyperV2 with CommandLineGATKArgs val indel = new IndelGenotyperV2 with CommandLineGATKArgs
indel.input_file :+= bam.toNamedFile indel.input_file :+= bam.toNamedFile
indel.out = swapExt(bam,".bam",".indels.vcf") indel.out = swapExt(bam,".bam",".indels.vcf")